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BioModels MODEL2407300002 Sponge Holobiont Network

Community ID CommunityMech:000013
Ecological State STABLE

BioModels record MODEL2407300002 provides simulations and model assets for an eight-species sponge microbiome network, modeling interactions among symbiont clades in a Stylissa holobiont.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Ammonia-oxidizing archaea — ontology label: Archaea NCBITaxon:2157 · TaxonMech · TraitMech
PRIMARY_PRODUCER
N/A
  • PMID:39738126 - PARTIAL (COMPUTATIONAL)
    "constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp."
Nitrite-oxidizing bacteria — ontology label: Bacteria NCBITaxon:2 · TaxonMech · TraitMech
PRIMARY_PRODUCER
N/A
  • PMID:39738126 - PARTIAL (COMPUTATIONAL)
    "constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp."
Novel cross-feeding bacterial taxon — ontology label: Bacteria NCBITaxon:2 · TaxonMech · TraitMech
CROSS_FEEDER
N/A
  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "the key role that a newly discovered bacterial taxon has in cross-feeding activities"

Ecological Interactions

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

Ecological interaction network for BioModels MODEL2407300002 Sponge Holobiont Network Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Cross-feeding
Other

Coupled Nitrification in Stylissa Holobiont

CROSS_FEEDING

COMPUTATIONAL - archaeal ammonia oxidation supplies nitrite to the modeled nitrite oxidizer, enabling coupled nitrification. This is predicted cross-feeding, not evidence that thermodynamically obligatory substrate removal links the partners. A nitric-oxide-forming reaction was disabled to approximate extracellular chemistry; modeled exchanges are not measured holobiont fluxes.

Metabolites: ammonia (CHEBI:16134 · MediaIngredientMech · CMMMech), nitrite (CHEBI:16301 · MediaIngredientMech · CMMMech), nitrate (CHEBI:17632 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Stable Ammonia-Supported Nitrifying Consortium

COMPUTATIONAL - nitrite generated by archaeal ammonia oxidation supplies the modeled nitrite oxidizer and can enable joint growth, conditional on imposed ammonia supply and cell removal. This substrate-support mechanism does not establish in-vivo stability or thermodynamic syntrophy.

Evidence

  • PMID:39738126 - PARTIAL (COMPUTATIONAL)
    "constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp."
  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "ammonia oxidation of C. stylissae was able to support the growth of N. stylissae"

Nutrient-Responsive Cross-Feeding Network

CROSS_FEEDING

COMPUTATIONAL - alternative organic-input regimes alter predicted exchanges among eight reconstructed Stylissa symbionts. Deltaporibacter contributes condition-dependent routes, not demonstrated active coordination of the community. HT denotes hypotaurine. Predicted exchange and net carbon balance share imposed inputs; the whole-network summary is not an independent cause of its component routes or trophic-balance summary.

Metabolites: organic molecular entity (CHEBI:50860 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "the key role that a newly discovered bacterial taxon has in cross-feeding activities"
  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "different organic inputs can result in net heterotrophy or autotrophy of the symbiont community"

Sponge-Derived Nutrient Provisioning to Microbiome

COMPUTATIONAL - metabolites enriched in sponge tissue were treated as candidate host-derived inputs to microbial models. Their host origin and delivery are assumptions informed by metabolomics, not resolved host-to-microbe flux. The host metabolism and respiration were not modeled, so this does not establish reciprocal host fitness or whole-holobiont mutualism.

Metabolites: organic molecular entity (CHEBI:50860 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Nutrient-Responsive Cross-Feeding Network

COMPUTATIONAL - supplying candidate host-derived organic substrates changes the resources available for modeled microbial exchange. This conditional input-to-exchange mechanism does not prove host secretion, reciprocal fitness or the same fluxes in vivo.

Evidence

  • PMID:39738126 - PARTIAL (COMPUTATIONAL)
    "constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp."
  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "Our models define the importance of sponge-derived nutrients for microbiome stability"

Stable Ammonia-Supported Nitrifying Consortium

COMPUTATIONAL - simulated ammonia supply and cell-removal rate jointly determine nitrifier growth and composition. The stability criterion divides the final AOA:NOB population ratio by its initial value and requires that normalized ratio to lie within 0.5-2; these are not absolute population-size bounds. The criterion and input regimes are model choices, not measured environmental thresholds or a separate syntrophic interaction.

Metabolites: ammonia (CHEBI:16134 · MediaIngredientMech · CMMMech), nitrite (CHEBI:16301 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "a stable and actively growing nitrifying community can only be achieved with ammonia concentrations"

Deltaporibacter Nitrogen-Linked Cross-Feeding

CROSS_FEEDING

COMPUTATIONAL - the Deltaporibacter stylissae reconstruction participates in nutrient-regime-dependent exchanges. Under hypotaurine input, predicted nitrate reduction supplies nitric oxide; combined organic inputs produce a different exchange pattern including acetate donation. These are conditional predicted fluxes, not measured transfer or evidence that this organism actively coordinates the microbiome.

Biological Processes:

Evidence

  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "Deltaporibacter stylissae within the Myxococcota, which appears in Stylissa sp. to be central in cross-feeding activities and nitrogen cycling"

Nutrient-Dependent Symbiont Trophic Balance

COMPUTATIONAL - alternative organic inputs change net carbon exchange of the modeled microbial symbionts between net heterotrophy and net autotrophy. This is an aggregate model endpoint, not itself an additional cross-feeding interaction. Host respiration is excluded, so the result does not classify the entire living sponge holobiont.

Metabolites: organic molecular entity (CHEBI:50860 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "different organic inputs can result in net heterotrophy or autotrophy of the symbiont community"

Associated Datasets

Dataset Type Repository Accession
Primary publication
Nature Communications article describing genome-scale metabolic modeling of Stylissa holobiont microbiome. 		OTHER OTHER doi:10.1038/s41467-024-55222-w
BioModels simulation resource
RDS simulation object for eight-species metabolic network. 		OTHER OTHER 8-species_network_simulations_HT_and_Laurate_100th_hr.RDS

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Do measured partner fluxes and host inputs validate the conditional sponge model mechanisms?

The eight reconstructions account for 98.3% of MAG-mapped reads, not all reads, and include merged MAGs and gap-filling. Candidate host inputs rely on tissue enrichment with two samples. Cell removal, death and ammonia inputs are imposed parameters; no simulation was rerun. Full cached main text/captions read, not images, supplements or model files. Three-domain roster reconciliation remains #1268.

Attaches to: ecological_interactions#Coupled Nitrification in Stylissa Holobiont, ecological_interactions#Nutrient-Responsive Cross-Feeding Network, ecological_interactions#Sponge-Derived Nutrient Provisioning to Microbiome, ecological_interactions#Stable Ammonia-Supported Nitrifying Consortium, ecological_interactions#Deltaporibacter Nitrogen-Linked Cross-Feeding, ecological_interactions#Nutrient-Dependent Symbiont Trophic Balance

External Resources

Name Repository Resource ID
BioModels entry
Sponge holobiont genome-scale interaction model resource. 		BIOMODELS MODEL2407300002
  • doi:10.1038/s41467-024-55222-w - PARTIAL (COMPUTATIONAL)
    "constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp."
PubMed record
Genome-scale metabolic modelling of Stylissa sponge holobiont interactions. 		OTHER PMID:39738126
  • PMID:39738126 - SUPPORT (COMPUTATIONAL)
    "different organic inputs can result in net heterotrophy or autotrophy of the symbiont community"

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

TaxonMech: Ammonia-oxidizing archaea ↗ TraitMech: Ammonia-oxidizing archaea ↗ TaxonMech: Nitrite-oxidizing bacteria ↗ TraitMech: Nitrite-oxidizing bacteria ↗ TaxonMech: Novel cross-feeding bacterial taxon ↗ TraitMech: Novel cross-feeding bacterial taxon ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗